\n\n\n\n\n\n\n## Use\n\n### API\n\nThe BIDS Validator has one primary method that takes a directory as either a\npath to the directory (node) or the object given by selecting a directory with a\nfile input (browser), an options object, and a callback.\n\nAvailable options include:\n\n- ignoreWarnings - (boolean - defaults to false)\n- ignoreNiftiHeaders - (boolean - defaults to false)\n\nFor example:\n\n`validate.BIDS(directory, {ignoreWarnings: true}, function (issues, summary) {console.log(issues.errors, issues.warnings);});`\n\nIf you would like to test individual files you can use the file specific checks\nthat we expose.\n\n- validate.BIDS()\n- validate.JSON()\n- validate.TSV()\n- validate.NIFTI()\n\nAdditionally you can reformat stored errors against a new config using `validate.reformat()`\n\n### .bidsignore\n\nOptionally one can include a `.bidsignore` file in the root of the dataset. This\nfile lists patterns (compatible with the [.gitignore syntax](https://git-scm.com/docs/gitignore))\ndefining files that should be ignored by the validator. This option is useful\nwhen the validated dataset includes file types not yet supported by BIDS\nspecification.\n\n```Text\n*_not_bids.txt\nextra_data/\n```\n\n### Configuration\n\nYou can configure the severity of errors by passing a json configuration file\nwith a `-c` or `--config` flag to the command line interface or by defining a\nconfig object on the options object passed during javascript usage.\n\nIf no path is specified a default path of `.bids-validator-config.json` will be used. You can add this file to your dataset to share dataset specific validation configuration. To disable this behavior use `--no-config` and the default configuration will be used.\n\nThe basic configuration format is outlined below. All configuration is optional.\n\n```JSON\n{\n\t\"ignore\": [],\n\t\"warn\": [],\n\t\"error\": [],\n\t\"ignoredFiles\": []\n}\n```\n\n`ignoredFiles` takes a list of file paths or glob patterns you'd like to ignore.\nLets say we want to ignore all files and sub-directory under `/derivatives/`.\n**This is not the same syntax as used in the .bidsignore file**\n\n```JSON\n{\n\t\"ignoredFiles\": [\"/derivatives/**\"]\n}\n```\n\nNote that adding two stars `**` in path makes validator recognize all files and\nsub-dir to be ignored.\n\n`ignore`, `warn`, and `error` take lists of issue codes or issue keys and change\nthe severity of those issues so they are either ignored or reported as warnings\nor errors. You can find a list of all available issues at\n[utils/issues/list](https://github.com/bids-standard/bids-validator/blob/master/bids-validator/utils/issues/list.js).\n\nSome issues may be ignored by default, but can be elevated to warnings or errors.\nThese provide a way to check for common things that are more specific than BIDS\ncompatibility. An example is a check for the presence of a T1w modality. The\nfollowing would raise an error if no T1W image was found in a dataset.\n\n```JSON\n{\n\t\"error\": [\"NO_T1W\"]\n}\n```\n\nIn addition to issue codes and keys these lists can also contain objects with\nand \"and\" or \"or\" properties set to arrays of codes or keys. These allow some\nlevel of conditional logic when configuring issues. For example:\n\n```JSON\n{\n\t\"ignore\": [\n\t\t{\n\t\t\t\"and\": [\n\t\t\t\t\"ECHO_TIME_GREATER_THAN\",\n\t\t\t\t\"ECHO_TIME_NOT_DEFINED\"\n\t\t\t]\n\t\t}\n\t]\n}\n```\n\nIn the above example the two issues will only be ignored if both of them are\ntriggered during validation.\n\n```JSON\n{\n\t\"ignore\": [\n\t\t{\n\t\t\t\"and\": [\n\t\t\t\t\"ECHO_TIME_GREATER_THAN\",\n\t\t\t\t\"ECHO_TIME_NOT_DEFINED\"\n\t\t\t\t{\n\t\t\t\t\t\"or\": [\n\t\t\t\t\t\t\"ECHO_TIME1-2_NOT_DEFINED\",\n\t\t\t\t\t\t\"ECHO_TIME_MUST_DEFINE\"\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t]\n}\n```\n\nAnd in this example the listed issues will only be ignored if\n`ECHO_TIME_GREATER_THAN`, `ECHO_TIME_NOT_DEFINED` and either\n`ECHO_TIME1-2_NOT_DEFINED` or `ECHO_TIME_MUST_DEFINE` are triggered during\nvalidation.\n\n\"or\" arrays are not supported at the lowest level because it wouldn't add any\nfunctionality. For example the following is not supported.\n\n```JSON\n{\n\t\"ignore\": [\n\t\t{\n\t\t\t\"or\": [\n\t\t\t\t\"ECHO_TIME_GREATER_THAN\",\n\t\t\t\t\"ECHO_TIME_NOT_DEFINED\"\n\t\t\t]\n\t\t}\n\t]\n}\n```\n\nbecause it would be functionally the same as this:\n\n```JSON\n{\n\t\"ignore\": [\n\t\t\"ECHO_TIME_GREATER_THAN\",\n\t\t\"ECHO_TIME_NOT_DEFINED\"\n\t]\n}\n```\n\nFor passing a configuration while using the bids-validator on the command line,\nyou can use the following style to for example ignore empty\nfile errors (99) and files that cannot be read (44):\n\n```\nbids-validator --config.ignore=99 --config.ignore=44 path/to/bids/dir\n```\n\nThis style of use puts limits on what configuration you can require, so for\ncomplex scenarios, we advise users to create a dedicated configuration file with\ncontents as described above.\n\n### In the Browser\n\nThe BIDS Validator currently works in the browser with [browserify](https://browserify.org/)\nor [webpack](https://webpack.js.org/). You can add it to a project by cloning\nthe validator and requiring it with browserify syntax\n`const validate = require('bids-validator');` or an ES2015 webpack import\n`import validate from 'bids-validator'`.\n\n### On the Server\n\nThe BIDS validator works like most npm packages. You can install it by running\n`npm install bids-validator`.\n\n### Through Command Line\n\nIf you install the bids validator globally by using `npm install -g bids-validator`\nyou will be able to use it as a command line tool. Once installed you should be\nable to run `bids-validator /path/to/your/bids/directory` and see any validation\nissues logged to the terminal. Run `bids-validator` without a directory path to\nsee available options.\n\n## Docker image\n\n[](https://hub.docker.com/r/bids/validator)\n\nTo use bids validator with [docker](https://www.docker.com/), you simply need to\n[install docker](https://docs.docker.com/install/) on your system.\n\nAnd then from a terminal run:\n\n- `docker run -ti --rm bids/validator --version` to print the version of the\n docker image\n- `docker run -ti --rm bids/validator --help` to print the help\n- `docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data`\n to validate the dataset `/path/to/data` on your host machine\n\nSee here for a brief explanation of the commands:\n\n- `docker run` is the command to tell docker to run a certain docker image,\n usually taking the form `docker run ![\"\"/](\"https://avatars.githubusercontent.com/u/3460267?v=4?s=50\")
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